I have installed Fedora official pymol package 18.104.22.168-3.20120218svn3982.fc17. And all is good except that pymol is ignoring modifier keys like Shift and Ctrl. I also have downloaded latest source from sourceforge (not svn) and compiled it, and I found the same problem. I also tried older version of pymol (1.4.1) but again I found the same problem.
I use ibus, so I also tried turning it off by im-chooser, removing "export QT_IM_MODULE=ibus" and "export GTK_IM_MODULE=ibus" from .bashrc, and logging off and back on. Still I had the same problem.
Have some GLUT key constants changed over time? Where should I look?
I investigated into it a little.
when freeglut is available, p_glutGetModifiers() that is called by MainButton() defined in layer5/main.c becomes an alias of glutGetModifiers() declared in GL/freeglut_std.h, as directed by layer0/os_gl.h.
but this function is returning zero even if modifier key was pressed. I inserted fprintf(stderr,"watch:%d\n",glutGetModifiers()); into MainButton() and compiled pymol and got zeroes.
I don't know if freeglut is being incorrectly used in the pymol source. but otherwise the root of this problem is deeper...